I am testing a 10x fastq dataset , but cellranger count complains "An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input", I have tried all the chemistry recommendation codes on the 10x genomics website, and I still get the same result, how can I solve this problem, thanks.
Answer from @maximilian-press, converted from comments:
I can't comment on 10X data specifically, however, I suggest writing a simple script or command that counts the frequency of each barcode, and reports back the N (10? 20? 100?) most frequent ones, which will allow you to investigate in more detail. This is what I have done in the case of suspected bardode swaps or reverse complement issues.